yes it is. The panel tool is a bot that sends changes to the server with elevated privileges, the server does not send changes made locally/manually back to the panel.

Certain functions that you carry out can only be done from the panel, because they are administrative. Others, were you as owner, have permission at the command prompt the panel will not know

One example is crontab, the panel tool is there for people unfamiliar with the command prompt and creating a crontab file. But if you do it from the shell prompt using the crontab command the panel will not know about your manually submitted and running cron.

But if I create a database with the panel, shouldn’t I see it also when I do a ‘show databases’ command? I understand the panel can be unaware of some stuff, but a ‘show databases’ should see everything…

I have a database created using the panel. When I connect with SSH and issue the command ‘show databases;’, the database is not in the list.

Here is what I did, but I’m not sure if it is important. It will certainly be clearer though.

Initially, the database was created using the wordpress automatic installation.
I finally decided to remove everything and reinstalled manually. I did :
–> mysql -u username -p -h hostname
–> drop database dbname;
Seeing that the panel hadn’t been updated, I decided to delete it in the panel too.
Afterwards, I restored the database, but now it is not showing when I do :
–> mysql -u username -p -h hostname
–> show databases;

Creating and destroying databases in the Panel is mainly about controlling your MySQL users’ permissions to that database, not actually creating / dropping the database itself. We do create a database when you first add it, but beyond that it’s largely kept in whatever state you left it. In particular, the MySQL recycle bin works because we don’t drop databases immediately when you remove them in the panel. (We keep the databases around, with no permissions, for a few extra days.)

If you’ve dropped a database through the MySQL command line, it’ll stay dropped until you create it again, using something like: